# REVISION 2.0: Quantum Coherence Model for Periodontal LLLT

**DOI:** `10.7910/DVN/THCRB2`  
**Revision Date:** [CURRENT DATE]  
**Version:** 2.0 (Revised and Corrected)  
**Manuscript:** "A Computational Quantum Dynamical Model for Periodontal Low-Level Laser Therapy: Coherence and Excitation in a Biologically Contextualized Framework"

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## 📋 TABLE OF CONTENTS

1. [Revision Overview](#-revision-overview)
2. [What Changed & Why](#-what-changed--why)
3. [File Structure](#-file-structure)
4. [File Descriptions](#-file-descriptions)
5. [How to Verify Results](#-how-to-verify-results)
6. [Reproduction Instructions](#-reproduction-instructions)
7. [Parameter Details](#-parameter-details)
8. [Citation](#-citation)
9. [Contact & Support](#-contact--support)

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## 🔄 REVISION OVERVIEW

This repository has undergone **significant revision** to address critical issues identified during peer review of the associated manuscript. The original Version 1.0 contained simulation data with unit inconsistencies and implementation errors. 

**Version 2.0 replaces all simulations with exact analytical solutions** that are mathematically rigorous, physically consistent, and fully reproducible.

### Key Improvements:
- ✅ **Unit consistency**: All frequencies in MHz, times in µs
- ✅ **Analytical verification**: Exact quantum mechanical formulas
- ✅ **Data quality**: Only physically valid parameters
- ✅ **Reproducibility**: Complete reproduction script provided
- ✅ **Transparency**: Full formula derivations documented

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## ⚠️ WHAT CHANGED & WHY

### Issues in Version 1.0:
1. **Unit inconsistencies**: Mixing of normalized units with physical scales
2. **Implementation errors**: Incorrect collapse operators in simulation code
3. **Non-physical fits**: Invalid coherence decay parameters in Table 2
4. **Statistical overreach**: Inappropriate regression analysis

### Corrections in Version 2.0:
1. **Analytical approach**: Replaced simulations with exact formulas
2. **Clear scaling**: Γ = 1 MHz → 1 normalized unit = 1 µs
3. **Validated fits**: Only physically reasonable coherence decays (τ = 10-40 µs)
4. **Formula-based**: Used standard quantum optics results instead of regression

### Preserved Elements:
- Same research questions
- Same clinical parameters
- Same interdisciplinary vision (quantum physics + periodontology)
- Same parameter ranges (Ω = 0.05-0.5 MHz, γ = 0.05-0.2 MHz)

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## 📁 FILE STRUCTURE
